tag:notobiotica.posthaven.com,2013:/posts noto|biotica 2017-09-14T01:14:16Z noto|biotica tag:notobiotica.posthaven.com,2013:Post/1191075 2017-09-14T01:14:16Z 2017-09-14T01:14:16Z Taxonomy 2028 Challenge: Knowing the origins of the Australian biota

By the year 2028 we will have compiled a database of information on the origin of Australia’s biota. This database will detail the area of origin for every genus within Australia, and the timing of its original arrival in Australia.

Initially, the database could be compiled from published phylogenetic data, eventually being replaced with phylogenetic information which has been analysed in a consistent methodology.  This goal could be achieved through the targeted sampling and molecular sequencing of lineages that have distributions spanning Australia and neighbouring landmasses (Southeast Asia, the Pacific, Antarctica, etc.) and then of lineages with more cosmopolitan distributions. This database will establish an understanding of the unique and varied evolutionary history of the Australian biota, determining which lineages are ancient Gondwanan relicts and more recent immigrants, as well as identifying spatio-temporal patterns of immigration, emigration and diversification in the history of the assembly of the Australian biota. It would also provide an invaluable resource for the advancement of research in Australian biogeography, biogeography theory, invasive species ecology, geology, palaeontology, evolutionary theory, trait evolution and ecology and for informing conservation priorities and strategies.

This phylogenetic information could be integrated into the ALA platform through the addition of interactive phylogenies on each taxon’s ALA page. Clicking on nodes of each phylogeny could show biogeographic, morphological trait and divergence age data for that taxon. Publication of phylogenetic information in such an interactive way would engage the public and raise understanding of the significance of the unique evolutionary histories of groups within the Australian biota. It would provide an alternative visual mechanism for exploring taxa by placing them in a phylogenetic context. It would also provide a platform through which evolutionary concepts are made accessible for lay people, encouraging the the exploration of integrative evolutionary questions and engaging them with concepts in systematics, evolution and taxonomy.

Lizzy Joyce
PhD Candidate - Australian Tropical Herbarium & James Cook University
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tag:notobiotica.posthaven.com,2013:Post/1189861 2017-09-08T23:46:22Z 2017-09-08T23:55:43Z Linneaus and the Ackronyme project (satire)

The following fragment was pieced together from notes written by Jakob Rindler and only recently discovered in a shed at the Liverpool Botanic Garden. It is thought the notes were acquired, together with many other documents and specimens from the Linneaus estate, by Sir James Smith in 1783.

Although not an "apostle" student of Linneaus, Rindler was a summertime house-guest at the Linneaus farm at Hammarby, now a suburb of Uppsala. In the early 1760s a botanic garden was planted at Hammarby, and in several letters from Linneaus, Rindler is mentioned as a young and enthusiastic botanist who was of great help in tending the Hammarby plantings.

Judging from internal evidence, the meeting reported by Rindler probably took place in 1764 or 1765. It is curious that Linneaus never mentioned the interview with Sir Edward Ackronyme in later correspondence.

I have taken the liberty of translating Rindler's notes into reasonably modern English.

***

The master was visited today by an English gentleman, Sir Edward Ackronyme, who carried letters of introduction from Earl Macclesfield [Royal Society of London] and Philip Miller [Chelsea Physic Garden].

The gentleman appeared to be very intelligent and spoke both Swedish and Latin. He praised the master's many contributions to knowledge. He said the master was a scientific colossus of the age and respected by all who knew the master's work. He said famam extendere factis [through our deeds we extend our fame] on the master's coat-of-arms was an inspiration to all natural philosophers.

The gentleman said he had read the second edition of the master's Species Plantarum, and had observed that it was supplemented with corrections to the text and with additional notes. The gentleman had a proposal to make in connection with this.

He proceeded to describe correctly and in interesting detail how Species Plantarum had been written and published, which greatly surprised the master. The gentleman said that his proposal did not, however, concern the production of scholarly books, but instead the use and diffusion of the knowledge in the books.

The gentleman explained that he and others had invented a method for reproducing the master's descriptions, using a large number of scribes and a new means of printing which was very swift and not expensive. The words of the master concerning individual species would be copied out by the scribes and printed in large numbers as separata.

The separata might then be sold more widely than the Species Plantarum. The gentleman gave an example, in which a philosopher in Virginia could acquire the descriptions of plants and animals native to Virginia. The two volumes of Species Plantarum contained many descriptions of plants and animals which were not found in Virginia and might not be of interest to philosophers there. The separata pertaining to Virginia, or to any other place, could be gathered up and placed in a pouch.

The gentleman said that if a purchaser was only interested in Pisces in the master's Systema Naturae, then the separata for Pisces could be gathered together for the purchaser.

The master observed that this was very clever. At this point the gentleman asked the master if the master could see value in this method of diffusion of knowledge. The master replied that it indeed had value.

The gentleman was pleased to hear this, and said that he had also received encouraging replies to this question from other philosophers. The gentleman had spoken directly to Dr Scopoli in Idrija and to other philosophers who had published works of natural history. Each had agreed that there was much merit in the idea of spreading more widely their descriptions and classifications.

The gentleman said that if the master wished to make a correction or addition to any one of his species, that information could be sent to the scribes, who would make the correction or addition in a new separatum. The new separatum would be sent to all those who had purchased an uncorrected version. The gentleman said this was possible because the cost of printing separata by the new method was hardly of consequence, and the number printed could be one or a thousand.

The gentleman produced a small sheet of paper and gave it to the master. On the paper had been printed a description from Species Plantarum of a species, and beneath the description was the name of the master. Beneath the name was an addition the master had made to the description, and this too was subscribed with the name of the master. At the bottom of the paper was a date, which the gentleman said was the date on which the separatum had been printed.

The master again praised the cleverness of the idea of separata. He begged leave to ask questions, and the gentleman agreed.

The master asked first whether there would be a cost to himself in the production of separata. The gentleman said there would be no cost to the master or to other philosophers. The work of the scribes and the printing of separata would have royal patronage. He was not presently permitted to name the royal courts from which the patronage would come.

The master expressed surprise to hear that more than one kingdom was offering to assist. The gentleman explained that the idea of diffusion of knowledge through separata was not his alone. He was one of a group of interested gentlemen distributed throughout Europe. Each member of the group made a particular contribution. His own contribution related to printing, regarding which he could modestly admit to having acquired a degree of expertise.

The group of gentlemen met on occasions in various European cities. Their next meeting would take place in Paris. They would consider the question of whether separata should be printed only in Latin, or also in various modern languages, and if the latter, whether one separatum should be printed in more than one language. The gentleman said there were arguments for and arguments against, and the question might have to be resolved at a later meeting in another city.

Now the master asked, whether the patronage enjoyed by the gentlemen could be extended to natural philosophers and their students. The gentleman apologised because he did not think it possible. The production and distribution of separata was a matter of diffusion of knowledge, not of the generation of knowledge. The gentleman said that he and the other gentlemen greatly appreciated the work done by the master and other natural philosophers. It was the humble role of the gentleman and his associates to spread that knowledge and to make it more useful.

At this the master became upset and spoke severely. He said he worked day and night on the investigation of a science that a thousand men will not be able to complete, to say nothing of the time he squandered every day on scientific correspondence, while the gentleman and his colleagues can constantly enjoy the amenities of life. The master said that separata may indeed be of value, but they add nothing at all to knowledge, and that the gaining of knowledge was his constant goal.

The gentleman said that he hoped nothing he had said had angered the master, and that he had one more question to ask. While the scribes were skilled and diligent, it occasionally happened that a copying error was made when producing the separata. The gentleman asked whether the master would be willing to examine drafts of separata before they were printed. He explained that he and his associates were not natural philosophers, and that natural philosophers would be the persons best able to locate and correct any errors.

This concluded the meeting with the gentleman. The master did not reply to the last question, but wished the gentleman a good day, and turned to me and said that there was work to be done in the garden.

- Bob Mesibov


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tag:notobiotica.posthaven.com,2013:Post/1189366 2017-09-08T22:20:52Z 2017-09-08T22:20:52Z A Dream of Invertebrate Utopia

I am continually impressed by the diversity of views and proposals for the Decadal Plan coming from different parts of the taxonomic community in Australia.  The project has brought some quite disparate communities together to discuss common goals as they have never done before.  

More and more I see the broader taxonomic community divided into two camps, those that are working on less diverse and relatively well-resourced taxonomic groups, and those that are working on very diverse but relatively poorly resourced groups.  Taxonomic groups don't switch between these camps, it is destiny, so resourcing differences become magnified and accentuated over generations and centuries.  

There has now be come such a huge divide between the "haves" and the "have-nots" that it has become a challenge in and of itself.  Much as rising income disparity is now seen as a major challenge for western democracies.  The differences between the "haves" and "have nots" are now so profound that priorities and solutions are often different depending on the camp the particular idea originated in.  I think it is also important to acknowledge the illogical, emotionally-driven and innately human process by which taxonomic groups end up in the "have" or "have not" category.  You could logically conclude that resources available to western science for taxonomy have only ever really scaled to the small groups of obvious macroscopic organisms, such as vertebrates and others, together representing just 5% or so of species.

The large and random differences in our taxonomic knowledge of different groups has a negative impact on biology generally.  It hampers any study that attempts to examine communities or ecosystems from a process or systems perspective.  We know some macroscopic species well, but are ignorant of species to which they are intimately connected and critically dependent, simply because those connected species happen to belong to one or more "have not" taxonomic groups.  

I wrote this little satirical piece of whimsy that imagined one of the "have not" groups, the weevils (Curculionoidea: Coleoptera), historically had been included as one of the "have" groups.  Hopefully it will cast some light on the different resource levels available to the "haves" and "have nots". I think we need to fully appreciate the challenges these institutional and resourcing differences have stamped on our communities before we can move forward together.

 

A Dream of Invertebrate Utopia

With satirical apologies to George Orwell’s Animal Farm

 

I don’t know how it all started, perhaps back in the 1700’s naturalists imagined that there were as many weevils as all other animals and plants, but that is not really my concern.  Quibble with the numbers, we now estimate that there are around 20,000-25,000 weevil species here, and they make up about 5% of Australia’s biota, in other words we have about as many weevil species as butterflies and moths, or plants. As we intensify our focus, we are discovering more and more new Australian weevil species.

Our scientific community studies weevils (Curculionoidea) because they are extremely diverse and occur all over Australia.  They are ecologically important, some species are pests, others are biosecurity threats and yet more are biological control agents.  You can walk into any Australian environment from the wet rainforests to the arid inland, and find a unique community of weevils.  Weevils first appear in the fossil record 160 million years ago, and Australia is home to some of the early branching lineages.  Our weevil fauna includes giant Eurhamphus that feed exclusively on southern hemisphere pines. Weevils are some of the most damaging pest of timber and stored grain, so understanding weevils is vitally important for our economy. Besides that, they are cool! 

Right back at the beginnings of the development of each state, and in the commonwealth, we set up large institutions devoted to the study of weevils, called Weevilariums.  These institutions are going strong today each with 20-30 paid staff beavering away studying the taxonomy, biogeography and phylogeny of Australia’s weevils.  And the good news is we are getting ever so close to finishing the job!

Each state Weevilarium has worked hard over more than a century on the taxonomy of the weevils from their state.  You really can gather some momentum with that sort of workforce over that many generations.  First we produced hard copy book series called Weevils of NSW, etc.  Turns out that we worked so hard in each state we had described many species more than once - especially those that cross state boundaries.  But that doesn’t matter-why just deliver when you can overdeliver, I say!  Now we are putting all the weevil treatments together electronically with commonwealth funding, and we really are going to have to sort out those overlaps once and for all.  Kind of a victory lap. Thank goodness for forward planning!

The Australian Weevilariums are incredibly well connected globally, and we even have set up a bespoke international code of nomenclature just for weevils!  Nothing like a specialist tool for a specialized job.  Now the codes for weevils and the remaining biota have diverged quite a bit, like Spanish and Portugese.  Sometimes if you know one you can read bits of the other, but if people are talking nomenclature the two systems are incoherent!

Thanks to commonwealth weevil digitization funds, we now have almost all 10 million weevil specimens in the Weevilariums databased, we have developed great lists of all the weevil species in each state.  We are making great headway in imaging all weevil type specimens.  We can now map and model weevil distributions with great accuracy, and search for areas of endemism and high species diversity with great sophistication.  We have very detailed information on weevil abundance, and have listed many species as rare and threatened with the appropriate authorities.  Weevil conservation biology is now an expanding field, generating large amounts of external income for the community. We even had a Weevil Liason Officer position at the Natural History Museum in London for more than 50 years sorting out the curly issues to do with weevil type specimens in European museums.

We now have a great self-sustaining system with academics at universities studying weevil taxonomy, teaching courses in weevil taxonomy and biology, churning out PhD graduates that can take positions at the Weevilariums. Our Australian Systematic Weevil Society meetings are attended by more than one hundred engaged professionals and students each year. We even have our own special weevil subcommittee to assess and recommend commonwealth funds for weevil taxonomy.  Nothing like having real experts making the big decisions! Probably something like 40% of the resources available for taxonomy in Australia are now devoted to weevils. 

Weevil larvae eat plants, but we are so busy studying weevils that we rarely take samples of the plants they are feeding on.  Early on in my career I took a few samples to the grumpy old retired guy who passes for our Australian plant taxonomy expert.  I had to keep badgering him for the ID’s, and after a few months he said none of the plants were described anyway.  Bit of a waste of time, but I did at least give him a chance!

We even have a number of weevil egg banks dotted around the country.  Weevil eggs are in demand because they are used in biological control programs both here and overseas.  In Canberra we have an egg bank for small weevils, a separate egg bank for big weevils, and there is another one for weevil eggs of all sizes just outside of Sydney.  We are planning brand new facilities for the two Canberra egg banks.  You can’t have enough new weevil egg banks, I say!

Looking back over the field it is clear that the high level of investment in weevil taxonomy has given us a huge head start in comparison to the taxonomic knowledge of almost every other group.  I suppose we really could learn more about weevils place in ecosystems if we knew a little more about the plants they feed on, for example.  It would also help with their conservation as well.  I guess weevils are really a boutique slice (5%) of our biodiversity. But what a great example we have provided for the communities studying other taxonomic groups to follow!

Our real focus these days is the tiny (0.5-1.0 mm long) black and brown weevils.  I don’t know what we will do once we have finished the taxonomy of Australia’s weevils.  Maybe move on to the Cerambycidae (longicorn beetles), another hugely diverse, ecologically important, related group.  But there is a lot to be said for just sticking to weevils.  With grand institutions to fill, new technologies and theories to apply, we may never finish!

   

Then I woke up, and reality dawned on me.  There are no Weevilariums in Australia or the world.  There is one professional weevil taxonomist working here on our fauna of 20,000-25,000 species.  Our weevil taxonomist is entirely supported in the Australian National Insect Collection by a generous bequest of millions of dollars from a philanthropist.  Without this gift there would be precisely no weevil taxonomists in Australia. Our weevil taxonomist is expected to revise a large chunk of the Australian weevil fauna during his career, as well as provide continuing advice in biosecurity and pest management.

With this level of investment we will never know the weevil fauna of Australia in any coherent time frame, and we invest even less in the study of almost every other comparably-sized invertebrate group.  I have chosen weevils as the subject of this satirical piece for convenience, any number of other comparable invertebrate groups could substitute.
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tag:notobiotica.posthaven.com,2013:Post/1188937 2017-09-05T11:55:45Z 2017-09-11T04:37:38Z Counting species - questions and meta-questions

Yet another paper has come out (Larsen et al. "Inordinate fondness multiplied and redistributed: The number of species on earth and a new pie of life" The Quarterly Review of Biology 92(3): 229-265, 2017) asking the perennial "how many species are there on earth" question.

This is potentially an important question, and potentially a non-question. The question (whether it's important or not a question) is in turn important for the decadal plan, but also more broadly for biology as a whole. I'll return to the decadal plan later.

This issue is a problem, because current estimates for the number of species on earth vary from ~2 million (see refs in paper above) to ~1 trillion (I don't even really know how big a trillion is, but it's much bigger than 2 million). The paper above takes a stab in the dark (the authors would dispute this) and puts the figure at 1–6 billion. 

Take your pick. That's our problem. The number can be almost anything you want it to be.

But I think there's a bigger problem, which is that none of the studies that make these estimates ask what I think is the most important question, which is: does the how-many-species question make any sense? (Or more precisely, is the question answerable? The studies assume that it is, without justifying this assumption.) 

This is a meta-question, a question about a question. Until we can answer the meta-question, trying to answer the question is almost certainly futile. Let me explain; but first, let me digress to the late 18th Century.

At that time, some of the most influential French scientists (Jussieu, Adanson, De Candolle) had an important argument about the "shape" of nature. Jussieu (one of the leading scientists in the post-Linnaean world) argued from first principles that nature was continuous. He believed that somewhere out there (and increasingly being discovered during the great age of exploration) existed an intermediate form between every recognised taxon. There would be found organisms that would bridge the apparent gap between all species, between all genera, all families, all orders etc. Nature, in Jussieu's view, would prove to be a complete continuum, and taxonomy would eventually become an utterly arbitrary division of that continuum, just as colour terms arbitrarily divide the spectrum of visible light. Jussieu, by the way, was perfectly comfortable with this.

Adanson and De Candolle, by contrast, believed that the gaps observed between clusters of closely similar organisms were real, and that a relatively non-arbitrary ("natural") taxonomy could be based on the identification of these gaps. What's more, they believed that the cluster-and-gaps pattern could be discerned at all taxonomic levels, allowing us to create a natural classification of species, genera, families etc.

Adanson and De Candolle won. Nature was found to be inherently gappy; they had invented a (non-algorithmic) form of the phenetic method; and a century-and-a-half of a "taxonomy of the gaps" ensued.

Phylogenetics has slightly changed our views on all this, but only slightly. We're now interested in clades and all that, of course, but (at least at species level) we're still very keen on gaps. We now use terms like coalescence; the issue may take the form of working out what percentage difference between two barcodes is required to infer two species; it's still about gaps.

But - what if Jussieu was right? Not exactly right in the sense that there is a continuum of forms, but right in the sense that there's a continuum of gaps. What if there are big gaps (between e.g. a tuatara and its nearest relatives) down to small gaps (between two closely realted species) to smaller gaps (perhaps between "cryptic species") to very small gaps (the ones that the next generation of taxonomic splitters may use to ensure that taxonomy is a never-ending science, and that some orchid taxonomists use today - sorry, couldn't resist the dig). 

What does this mean to our question "how many species are there"? It may mean that the answer is whatever number you want it to be. Curiously, that seems to be about where we're at.

The problem can be rephrased in modern terms: is the pattern of variation in nature (call it its shape) fractal? A fractal pattern would be one where the pattern of "gappiness" is about the same all the way down. The gaps become finer and finer, but we can discern gaps all the way. If nature is fractal in this sense, then asking the question "how many species are there" is as meaningless as the classic fractal example "how long is the coastline of Australia?" There's no answer to that question. If you measure Australia's coastline on a 1:1,000,000 map you'll come up with one estimate; if you trace around every headland and minor prominence you'll get a much larger answer; if you trace around every grain of sand on every beach you'll get a larger answer still. In a fractal system, some questions are silly.

If, however, the shape of nature is non-fractal and there's a minimum observable gap, which we could use to objectively delimit species, then the question isn't silly at all (it's merely difficult).

So - I think we need to answer the meta-question ("Is the pattern of variation in nature such that the question of how many species exist is answerable?") before we try to answer the question ("how many species exist?"). An important question is - how could we go about answering the meta-question?

A thought experiment may help. Imagine that we had a full genome sequence of every individual organism on earth (no, I'm not suggesting this as a goal for the decadal plan). We could then use a super-super-computer to calculate the pairwise distances of every individual from every other individual, and plot these on a graph (increasing distance on the x-axis, frequency of that distance value on the y-axis). There would be a wide spread of pairwide distances on our plot, from close to zero to some arbitrarily large number. 

If the shape of nature is fractal, we'd see a complete spread of distance values with only random troughs and peaks; if, however, there's a real "species-gap", we'd see a distinct, non-random dip in the frequency distribution at some distance value somewhere closeish to the x-origin.

Our dataset would allow more sophisticated analyses. We could partition the data into different taxonomic groups (do we see a species-gap in, say, spiders as well as in bacteria, birds and plants - and importantly, if we do is it in the same place?). We could also partition into different ecological niches (do rainforest taxa have a gap in the same place as arid-zone taxa?; do r-strategists have a gap in the same place as K-strategists?), or breeding systems (do taxa that use sexual selection have a gap in the same place as taxa that don't?).

When you think about it, a graph like this would give us crucial insights, not only into the meta-question discussed here, but to help assess utility of e.g. barcodes for species delimitation. 

For what it's worth, my own guess is that we wouldn't see a magic value on a graph like this, but rather a random pattern of peaks and troughs all the way down. That is, my guess is that the question "how many species are there?" is a silly question.

Of course, like all good thought experiments, we could never do this. So this opens a new question - can we approximate the graph using real-world data sets? One possibility may be to use environmental genomic data - this has the advantage that it's presumably sampling sequences from every individual in the genomic soup, with no inherent taxonomic bias or pre-assumed taxonomy. I have no idea whether this idea has merit, and would be pleased to hear from someone who actually knows what they're talking about in this space.

One final question - do we try to deal with this issue in the decadal plan? We need to be careful about admitting that we have absolutely no idea how many species are in Australia and any estimate could be out by many orders of magnitude (this is not a great starting point for asking for funding to document our biodiversity). But we could argue for a project that addresses the meta-question, if indeed there's a way to address it. Now that would be a world scoop, I reckon.

As always, thoughts and comments very welcome.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1188640 2017-09-04T02:09:35Z 2017-09-05T00:07:09Z Roger Shivas

I am a mycologist and plant pathologist. My research interests are the systematics of fungi, especially those that cause diseases of plants and insects.

Currently I have two jobs, one as curator of the Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries as well as a professor (mycology) at the University of Southern Queensland.

Further information about the work that my colleagues and I do can be found at http://collections.daff.qld.gov.au

Dr Roger Shivas

Principal Plant Pathologist
Biosecurity Queensland
Department of Agriculture and Fisheries
GPO Box 267, Brisbane, Qld 4001

Tel. 61 7 3708 8478
Email: roger.shivas@daf.qld.gov.au

 

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tag:notobiotica.posthaven.com,2013:Post/1188225 2017-09-02T02:50:48Z 2017-09-02T02:52:25Z What about the passionate?

You've probably noticed: taxonomists aren't quite like other scientists.

They have a powerful fascination, if not an embarrassingly strong affection, for "their" groups of organisms. As the TV professionals say, they're great talent, because they talk excitedly on camera about their favourite taxa.

They study particular taxa for decades, becoming the experts — the "names" — to whom the biosecurity and agriculture sectors turn for advice.

They get better at what they do as time goes on. Taxonomists hit their stride in late career, peaking in their 50s and 60s and often publishing valuable papers in their 70s and 80s.

They can be relatively cheap to run. Unless they're focused on molecular systematics, the annual costs for their taxonomic work might amount to just a few thousand dollars.

They don't require a lot of formal training. Some of Australia's best taxonomists are self-taught in their specialty.

They can communicate with the public directly about ideas the public already understands: "species", "discovery", "natural habitats", "invasive organisms". Only rarely do taxonomists need a professional science writer to background and explain what they've done.

Granted all this, previous calls for more public support for taxonomy in Australia seem a bit misdirected.

There's the call for more training money in Australia's universities, which gave up teaching taxonomy long ago. Instead the universities turn out PhDs with only the dimmest understanding of the maths behind the sophisticated phylogeny-guessing software they've relied on, and a similarly limited understanding of their study taxon's biology. The door opens, the new PhDs leave and compete with all the other science PhDs for work, leaving behind an interest in the taxa that helped them get a degree.

There's the call for increased infrastructure spending on museums and herbaria, which is great, because taxonomists depend on collections. But if an increased collections spend isn't paralleled by increased taxonomic work in those collections, what's the point? Without more curators and supported visitors, museum managers are justified in asking "Why do you need more than one specimen of each species?" and "How is any of this bringing more people through our doors?"

There's the call for more IT spending to aggregate more collection and other species-tied data, and to put those data at the fingertips of... umm, somebody... with a browser. Who will then spend days cleaning the downloaded data because the IT funding included not one brass razoo for data cleaning at source (disclaimer: I'm a data auditor as well as a taxonomist).

What's missing from these calls? Any mention of the people we need more of, those passionate taxonomists.

Here are four ways those people could be encouraged and supported:

(1) Find them and train them: "We're looking for people who are absolutely fascinated with particular Australian life-forms, and we'll back your passion with taxonomic training. You may not get a career out of this, but we'll give you the tools for a lifetime of satisfying study and of contributions to knowledge of the Australian biota."

(2) Get the collections to reach out. Ensure that museums and herbaria have enough money to host taxonomist volunteers, and to sponsor short-term visits by specialists, including non-professionals.

(3) Reward productive taxonomic work. How about ABRS offering up to 50 $5000 annual grants per annum (up to $250 000 total) to currently publishing taxonomists, renewed every year? The money could be used for collection visits, field work, publishing fees, conference attendance and project-tied costs such as sequencing and SEM work. Unaffiliated and retired specialists would welcome even this small drip-feeding of taxonomic support. The risk per grant (the risk that the money is wasted) is trivial and easily minimised by cancelling payment if there's no evidence that productive taxonomic work was done in the preceding year.

(4) Pay for mentoring. There aren't any succession plans in Australian taxonomy, despite the fact that for every specialist there are dozens of non-specialists with an existing or potential interest in working with what could otherwise become an orphan group. We know those potential mentorees exist: the BowerBird project has brought hundreds of keen non-professionals out of the woodwork. Why not directly support the transfer of specialist knowledge, with travel grants for joint collection visits and field trips?

OK, it's obvious. I don't see taxonomy fitting entirely within an academic framework, which is how many taxonomy promoters want governments and other funding sources to see it. Instead I see taxonomy distributed widely within the Australian community, with weekend, holiday and retired collectors and enthusiasts being part of a broad collaborative effort. That's probably because I'm goal-focused. I want to see increased taxonomic effort in Australia, and that's not the same as an increased number of professional taxonomists.

- Bob Mesibov
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tag:notobiotica.posthaven.com,2013:Post/1188223 2017-09-02T02:41:01Z 2017-09-04T00:27:41Z Bob Mesibov

Bob Mesibov

I'm retired and I study millipedes.

Since 2002 (just before I retired) I've described or redescribed about 200 Australian millipede species. My Millipedes of Australia website is a resource for taxonomists and offers more than 14000 vetted locality records for named species as downloadable TSVs and KMLs.

In 43 years of collecting in Australia I've visited ca 3200 unique localities and deposited thousands of millipede specimens in museums in New South Wales, Queensland, Tasmania and Victoria.

I'm also a coder and data auditor, and spend a lot of my time happily working on the Linux command line.

For more about me and my Web resources, please visit polydesmida.info.


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tag:notobiotica.posthaven.com,2013:Post/1187953 2017-09-01T04:03:16Z 2017-09-01T04:03:16Z Taxonomy 2028 Challenge: 75% of species of Australian arthropods described by 2028

Posted on behalf of Penelope Mills, PhD candidate at The University of Queensland, working on the systematics and evolution of two groups of gall-inducing scale insects of Apiomorpha (Hemiptera: Eriococcidae).


By 2028 we will have described ~75% of species of Australian arthropods.

Arguably, phylum Arthropoda contains some of the most important species on the planet. They are also the most numerous group, and include about 80% of all the described species. However, much of the biodiversity within arthropods remain undescribed. Even within this current age of genomics, much of the research concerning Arthropoda focusses on a narrow breadth of species (e.g. medically-important species, agricultural pests, species of quarantine concern).

Many biodiversity surveys and estimates use species as the unit of measure. This means that better-known groups (e.g. chordates, angiosperms) are commonly included in biodiversity estimates, whereas the most numerous groups (e.g. Arthropoda) tend to be ignored because most species are yet to be described or can not be identified to species level.

There are already systematic grants available from ABRS and BushBlitz to nurture the discovery and documentation of Australia’s biodiversity. However, additional funding from government agencies, including the ARC, should be sought for funding basic taxonomic research to increase the achievability of the proposed goal.

The difficulty will be in convincing the funding panels and the public that this research is necessary and has far-reaching implications. Putting a name to a species allows it to be considered for biodiversity and conservation purposes, and the additional data provided by the description can be used by multiple digital platforms currently in place (e.g. Atlas of Living Australia, BowerBird) to examine additional questions about Australia’s biodiversity.


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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1187693 2017-08-31T02:09:26Z 2017-08-31T02:11:36Z Taxonomy 2028 Challenge: Using citizen surveillance applications to increase the number and frequency of culture collection samples for genomic analysis.

Posted on behalf of Andrew Taylor, PhD candidate Murdoch University and Research Officer DPIRD WA (andrew.taylor@dpird.wa.gov.au)


By 2028 genome sequencing will be common place amongst laboratories as technology improves and costs fall. This will result in more organisms having their genome sequenced and will lead to the taxonomic re-evaluation of a number of economically important plant pathogens. The oomycetes are one group of plant pathogens that are economically important to a diverse number of horticultural commodities and amongst natural ecosystems. In many instances they are also known to develop fungicide resistance rapidly, making control problematic. It appears from the number of oomycetes that have had their genome sequenced a taxonomic re-evaluation is likely.  

A characteristic of a number of oomycetes is that they are obligate biotrophs, meaning they can only be stored in culture collections on samples of the infected host. Often only a few of these representative samples exist and the collection dates are sporadic, in many cases multiple decades apart. This creates issues for researchers as it means samples lodged in collections are not allowed to be released as DNA extractions are considered destructive sampling. It also creates issues with biosecurity policy. With the likely taxonomic changes as a result of genome sequencing it will be difficult to gain access to old samples to be able to update prohibited organisms under re-evaluated classifications.

The proposal I put forward is to use the development of citizen surveillance applications that are being developed for a number of horticultural commodities across Australia to place call outs for samples of oomycete plant pathogens on a regular basis so that a greater number of culture collection samples can be submitted. A regular basis could be every 5 years or based on all diseases of a specific commodity using a similar timeline. Sample bags can be sent to responders with specific instructions to optimise collection and storage quality. Approaching the rural levy provider to fund the sampling and provide advertising would assist in costs associated with the sampling. 

The benefits of this proposal:

  • Provide enough samples in the collections to allow for DNA extractions without restrictions or as the technology improves.
  • Population data on a number of economically important plant diseases. This could be further used for:
    • Surveillance data for biosecurity purposes (includes nil results).
    • Genotypic information for fungicide resistance projects.
    • Information on the lineage of the disease over time, is it moving to more aggressive strains?
  • Allow citizens and industry to be included and feel invested in potential scientific research.
  • Cost effective way of collecting samples over a wide geographic area.
  • Cost effective for the levy providers as it would allow for long term collections rather than the boom and bust cycle of funding large scale projects. Often after large scale projects are completed the samples are destroyed meaning new projects spend money on recollecting samples.  
  • Provide information as to disease hot spots or location of prevalence over time.

This proposal could be broadened to a wider group of pathogens but I have written it from the basis of my PhD experience with oomycetes.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1187186 2017-08-29T01:40:56Z 2017-08-30T00:17:23Z Taxonomy 2028 Challenge: We need to database all specimens in the national collection, focusing on museum collections

When the Australasian Virtual Herbarium (AVH) was initiated in 1999, herbaria had for many years been databasing specimens. The AVH was seen as a logical progression from isolated specimen databases in each institution to an aggregated, national database of all specimens. Funding, obtained on the basis that the AVH would stimulate research including taxonomy, was obtained and used to complete the databasing of Australian specimens in all major herbaria, to mount and database backlog specimens, and to develop the AVH infrastructure.

Museums and other zoology (e.g. entomology) collections have also been databasing specimens for many decades. However, no museum collection is fully databased. OZCAM, the museum equivalent of AVH, is also an aggregation service, but museum collections have not had the benefit of a large, national, coordinated, funded campaign to database all specimens. This is a severe constraint on biodiversity inventory, mapping, biogeographic and ecological analyses in Australia.

By 2028 we will have databased half of all specimens in museum and other zoology collections, with a sustainable program to database all specimens within the following decade

Databasing museum and other zoology collections is a substantially bigger task than databasing all herbarium collections. The AVH includes >8 million records, comprising c. 80% of the estimated number of plant, algae and fungi specimens in Australian and New Zealand herbaria. OZCAM includes <4 million Australian records, comprising c. 6% of the estimated total number of specimens in Australian zoological collections. The task is large.

However, the benefits are also very large. The fact that the vast majority of zoological specimens are un-databased precludes us from doing simple tasks like drawing accurate distribution maps for most taxa, assessing the conservation status of taxa, determining where rare taxa occur and whether they occur in sites targeted for development such as mining or agricultural clearing. The AVH is now used by researchers all around the world for novel biodiversity analyses in areas ranging from evolution, ecology, biogeography and conservation, and has amply proven its value. A completed OZCAM would be even more valuable.

We now need to work out a way to invest the necessary effort into our zoological collections.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1187178 2017-08-29T00:31:45Z 2017-08-29T00:33:11Z Taxonomy 2028 Challenge: The view from an obligately biotrophic fungus

Posted on behalf of Professor Levente Kiss, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern Queensland

Prof. Kiss writes: As a newcomer in the Australian scientific community (I started to work here this year), I am deeply impressed by, and highly value, the Decadal initiative. During the past >25 years, I have been mainly interested in the biology, and taxonomy, of obligate biotrophic fungi, so I’ll focus on this group below.


We’d like you to scan the horizon, and share what you see.

It is an ‘easy’ assumption that during the next years more and more DNA loci will be used for taxonomic purposes. In fungal taxonomy, these new, or already exploited loci may not be useful for the whole Kingdom, and could be lineage-specific, as already shown in some cases by Schoch et al. (2012). (If interested, see my commentary about this paper: Kiss 2012). By the way, the identification of phylogenetically / taxonomically relevant lineage-specific DNA markers could be a general trend in future taxonomic works, within each Kingdom. Also, it is likely that whole genome analyses will be more widely used in taxonomic works, although this approach will always be limited by availability of funds, no matter how inexpensive will sequencing become, and methodology constrains, as well.

One aspect, which, in my opinion, has sometimes been forgotten, or at least neglected, especially in fungal (and, more generally, in microbial) ‘phylogeny only’ taxonomic works, is that, after all, different taxa have to be recognized as entities held together through gene flow. In obligate biotrophic fungi, where neither growth nor asexual and sexual reproduction are possible without being structurally and nutritionally linked to the living host tissues, gene flow cannot be envisaged if the respective fungi do not share the same hosts. However, in some groups of such strictly host-associated fungi, current practice is to apply the same taxon name for organisms that are unable to meet, and recombine, in/on the same hosts due to their narrow host specializations, but share identical, or highly similar, DNA barcode sequences. It has long been highlighted that gene phylogenies should not regarded as species phylogenies (Doyle 1992); however, the DNA barcode approach, as a quick-and-dirty method, has often been used in describing, for example, strictly host-associated taxa without taking in consideration obvious constraints in gene flow.

Where would you like taxonomy and systematics to be in a decade?

In obligate biotrophic fungi, when it comes to the future of taxonomy, my prediction is that their experimentally revealed host range, and, thus, the detection of whether gene flow is at all possible within a newly recognized taxon, will be much more considered during species descriptions, and will become a basic requirement in this process, in addition to developing better phylogenies for different taxa. Personally, I don’t think this approach can be skipped by whole genome analyses, as host specificity may be determined by a very small fraction of the genome, which may remain unrevealed when performing analyses of huge datasets.

What achievements or programs would you like to see in place? What milestones would you like us to pass?

I assume sequencing coupled with new DNA barcode developments, with direct taxonomic implications, will continue, and will always be fueled by the biotech sector. Specific taxonomic and/or biodiversity programmes (such as many more ABRS projects) focusing on those groups of organisms (in our case: fungi), which are challenging from a methodological point of view, and require specific approaches, in addition to the sequencing work, would lead to real breakthroughs in this field.

What innovations in technology, infrastructure, funding or organisation will make a big difference to your work and to our taxonomy and systematics?

I’d focus on the taxonomy of those groups of organisms (fungi) which are difficult to handle, due to their specific way of life (e.g., obligate biotrophs vs. free-living fungi). In taxonomy, personal expertise, special skills, are usually much more important than special infrastructure, therefore funding schemes should focus on key scientists and their students (i.e., salaries, fellowships), and should provide long-term support. In the USA, the NSF PEET scheme seems to be a great initiative to support taxonomic research, and especially training a new generation of taxonomists:

https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5451

References

Doyle JJ (1992) Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17: 144-163.

Kiss L (2012) Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl Acad Sci USA 109: E1811.

Schoch CL, et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109: 6241-6246.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1186422 2017-08-25T07:14:50Z 2017-08-25T07:14:50Z The Taxonomy 2028 Challenge: Validation of Australia’s vascular plant collection data

Herbarium collections are the primary source of verifiable data on Australia’s flora. The information associated with each collection — including the taxon name and its locality — underpins research across a broad range of disciplines. Thanks to advances in cyber-infrastructures and the development of novel bioinformatics tools and techniques, biodiversity and distribution data can now be explored and analysed within a phylogenetic and environmental framework, providing a greater evolutionary understanding of our flora and novel data to inform conservation planning. However, to maximise the outcomes of big data analyses it is imperative that we improve the quality of the data upon which these analyses are based.

Specimen identification errors are commonplace in herbaria and are not confined to taxonomic groups that lack a recent monograph — they also exist (to varying degrees) in groups that have been revised in the past 40 years, most notably in collections that have been made subsequent to a taxonomic treatment or have otherwise not been examined by the treatment’s author. Geocode errors (e.g. mistakes made at the point of data entry, miscalculations and labelling errors) are similarly rife, and can be extreme to relatively minor in magnitude.

Taxonomic and geographic errors in our biodiversity data reduce our knowledge of a taxon’s distribution and habitat requirements, result in the dissemination of inaccurate information to our stakeholders (e.g. incorrect distribution maps, wrongly identified voucher specimens and photographs), undermine the results and interpretation of phylogenetic studies and the accuracy of spatial analyses or environmental modelling, and may significantly impact conservation planning at the species or regional level. Furthermore, a significant amount of useful, high quality data remains inaccessible in specimen backlogs.

By 2028 all vascular plant collections in Australian Herbaria will be audited for taxonomic and geographic accuracy

The audit should include: a taxonomic assessment of all collections, with an emphasis on those that have not been verified by a taxonomic expert; cross-checking duplicates of a single gathering housed at different herbaria to ensure that they have matching identifications (and are therefore represented by just one dot on Australasia’s Virtual Herbarium); preparation, database and taxonomic verification of all backlog materials, including undatabased collections that are currently on loan to other institutions; and validation of locality and geocode information, particularly for all geographical outliers that have been taxonomically confirmed. It would be possible to value-add to this process by capturing information on the reproductive state of every specimen (i.e. whether flowering, fruiting or sterile) thereby informing future collection needs and phenological research.

An audit would lead to the discovery of new taxa and new populations of conservation-listed taxa. Indeed, many scientists are undoubtedly already aware of new taxa that are represented in herbarium collections but are not yet on the National Species List — this knowledge should be captured as part of this process, particularly if taxonomic publications are unlikely to be forthcoming in the short-term. 

An audit would improve the quality of data fundamental to our understanding of Australia’s biodiversity and its evolution. It would underpin the eFlora of Australia, enabling more accurate descriptions and distribution maps to be generated, and would improve the quality of derivative products such as regional or taxon specific Apps and field guides. An audit would have tangible conservation outcomes, providing better information for individual taxa and improving analyses directed at conservation planning and decision making, and would also reduce the amount of time required for data cleaning prior to a large-scale analysis.

Identification errors often arise from imperfect taxonomic knowledge and as such an audit of this nature could not be completely uncoupled from baseline taxonomic research; however, it would focus attention on future research needs (e.g. specimens, species or groups in need of further research could be flagged and prioritised; potential student research projects could be highlighted) and collection gaps.

We will need a significant number of skilled research scientists and identification botanists to conduct a taxonomic audit of collections at their home institution, collections originating from their home state but housed at other national herbaria, and specimens belonging to their taxonomic speciality groups. We will also need additional curatorial staff to database backlog material, validate questionable geocodes and localities, perform database edits and maintain existing collections (e.g. duplicates from other states). Staffing levels will need to be maintained into the future to ensure incoming collections are processed and verified without major delay.

Our collections underpin everything — let’s give them the attention they deserve.




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Juliet Wege
tag:notobiotica.posthaven.com,2013:Post/1186405 2017-08-25T04:37:33Z 2017-08-25T04:38:45Z Taxonomy 2028 Challenge: Collection and characterisation of parasites and symbionts alongside their hosts

Posted on behalf of Dan Huston - PhD Candidate, School of Biological Sciences, The University of Queensland


Organisms do not exist in isolation. Rather they exist in a web of complex associations with other organisms across space and time. Parasites and other symbionts are intimately associated with their host organisms and represent a massive component of global biodiversity. This component is mostly unseen, and rarely considered during biodiversity and ecological surveys or in conservation planning. Threats to biodiversity are amplified in parasite and symbiont populations, and host-specific lineages are likely to face extinction before their hosts. If we seek to characterise all of Earth’s biodiversity then, we must consider symbionts. Obviously, study of these organisms requires examination of their hosts, and therefore presents excellent collaborative opportunities for systematic biologists working on various groups. However, most parasites and symbionts have specific collection protocols required for producing specimens of a quality useful for taxonomy. Therefore I propose that:

By 2028, we will have established and implemented a collaborative support network dedicated to the collection and characterisation of parasites and symbionts, alongside characterisation of their hosts.

It could be called something that would result in a hip acronym like ‘Systematics of Symbionts and Parasites Support Network’ (SSAPSN). The major goal of the network would be to facilitate parallel host and symbiont collection efforts through coordinated collecting expeditions and training about parasite and other symbiont collection techniques. This will result in more impact per unit of collecting effort and more complete biodiversity collections in museums and other institutions for current and future research. Collaborative efforts between those systematic biologists studying hosts, and those studying the symbionts of said hosts may be seen as a better value for money and could increase grant application success, and may lead to cross-field citations of research papers. Most importantly, such efforts will give us a better understanding of life and the complex interactions between organisms in general.

Examples of the importance of considering parasites and symbionts in the future of taxonomy and systematics can be gleaned from many of the challenges already posted here on Noto | Biotica. Elaine Davidson’s challenge to explore the diversity and potential of microorganisms highlights the value these organism have to humans in terms of medicine, agriculture and industry. The many endosymbiotic microorganisms present in plants and animals are sure to provide novel chemical processes and enzymes of value to us. Kevin Thiele’s posts ‘every Australasian species genomed’ and ‘life in the late Anthropocene’ challenge us to collect tissue samples for all Australasian biota and sequence their genomes. While many of the tissue samples required are already in museums, such an endeavour will still require a huge collecting effort. These collecting events should be coordinated between systematic biologists across disciplines so that both host tissue and symbiont tissues can be collected concurrently. Nerida Wilson challenged us to double the number of described coral reef taxa by 2028. This topic hits close to home as much of my PhD research has been on coral reef parasites. We have only just begun to scratch the surface in terms of understanding parasite and symbiont diversity on the Great Barrier Reef and increased effort in characterising these organisms will greatly aid in doubling the number of described species for the region. Juliet Wege’s post ‘Obtain high quality collections of all undescribed vascular plant taxa’ highlights the difficulties inherent in acquiring these specimens from remote areas, and the need to execute targeted field expeditions to take advantage of seasonal weather conditions. Expeditions for rare plants could benefit from a nematologist to collect and study plant-parasitic nematodes and an entomologist to collect and study associated insects. A simple alternative would be training in the collection of these organisms for the botanists tasked with undertaking such expeditions. I fully understand that having collectors plan on collecting symbiont organisms alongside the stuff they are really interested in is a big ask, so including extra personnel on such expeditions focused on symbionts would be ideal. In the end however, any collection would be better than none.

The obvious first step towards building such a network is a level of organisation and a platform for communication. The existence of the SASB and now Noto | Biotica already gets us most of the way there. Noto | Biotica could be used as a news platform to help connect parasite and symbiont systematic biologists with those studying other groups, coordinate collection events, ‘wanted organism’ ads, etc. Because many parasites and symbionts are hidden in not so obvious locations in their hosts, and many require specialised fixation and preservation, workshops designed to train other systematic biologists in how to find these organisms and how to preserve them would be beneficial. Perhaps some small grants could become available for biologists undertaking collecting expeditions to cover the cost of extra field days and equipment to collect symbionts, or perhaps travel grants could be used to bring a parasitologist (we make for interesting dinner conversation) along on the trip. At the very least, a better awareness of all those organisms that exist under cover of their host is sure to lead to significant progress in the task of characterising all of Earth’s biota.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1186202 2017-08-24T12:57:01Z 2017-08-30T00:20:43Z Taxonomy 2028 Challenge: Let's digitally image all (or most) of our type specimens

 Posted on behalf of Kenny Travouillon, Curator of Mammalogy, Dept. of Terrestrial Zoology, Western Australian Museum


  1. By 2028 we will have digitalised the majority of type specimens in museum collections and made them available to researchers, industry and the general public.
  2. This will result in increased productivity of taxonomists, and make it easier to identify species in the field.  Several museums have already digitalised their type specimens and made them available on their website to the public, but achieving complete online access to all type data will help taxonomists recognise named species from new species more easily and also help create field guides, with keys to identify species in the field. This can not only be done for modern species, but also for fossil species, collected from more fragmented material.
  3. This matters because the taxonomic process is still a very slow process which requires years of research before making new species discovery. Yet, species are going extinct at an increasing rate, but many remain unnamed or have yet to be discovered. Digital access to type specimens will help speed up this process and get on with the job of conserving taxa earlier. Having a tool to make species identification in the field easier will also help researchers and industry with population monitoring. 
  4. Resources to achieve this will be funding to help institutions to hire additional staff to digitalise the collections, as well as IT staff to make this information available online for access by anyone. 
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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1185319 2017-08-21T05:25:59Z 2017-08-21T05:25:59Z The Taxonomy 2028 Challenge: Obtain high quality collections of all undescribed vascular plant taxa

New taxa continue to be discovered through examination of herbarium collections, regional surveys and botanical assessment of areas proposed for development; however, their taxonomic resolution and publication is often hampered by a lack of high quality (or even reasonable quality) material to serve as a type gathering or to enable the taxon to be adequately described. Many putative new taxa are represented by just one or a few collections that are fragmentary or lack key diagnostic features such as flowers or fruits.

By 2028 we will ensure that high quality collections of all undescribed vascular plant species (our known unknowns) will be made available for study in herbaria.

In the face of escalating threats to our biodiversity, there is a pressing need for a targeted collection effort to underpin taxonomic and systematic research, conservation planning and decision making. We need to act now or we risk undescribed species going extinct before they are adequately recorded. High quality collections can serve as type material and will enable reliable morphological descriptions to be generated, thereby facilitating accurate identification and on-ground conservation actions. Ancillary collections (e.g. samples for molecular studies, photographs, live material) could feed into other proposed 2028 goals (e.g. a genomic ark, stakeholder engagement) and ex situ conservation strategies.

For some undescribed species, obtaining good collections will be fraught with difficulties — many occur in remote or otherwise difficult to access areas, lack accurate geocode or locality information to enable them to be easily relocated, or require good seasonal conditions or fire to stimulate flowering. Furthermore, repeated visits to the same site may be required in order to collect adequate samples. We will therefore need skilled and energetic personnel to assess collection gaps, plan and conduct complex, targeted field expeditions or to otherwise co-ordinate regional personnel and skilled citizen scientists. Curatorial support will be essential for specimen processing, database and maintenance so that the specimens and their data can be made available for use by scientists.

An effort such as this would negate a major impediment to describing our vascular plant flora. And perhaps by the time this material is obtained, processed and ready for study, a future generation of skilled taxonomists with permanent positions will be in place and able to use these collections to best effect.


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Juliet Wege
tag:notobiotica.posthaven.com,2013:Post/1184571 2017-08-18T01:09:33Z 2017-08-18T01:21:24Z Taxonomy 2028 Challenge: A vision for fungal taxonomy and systematics

Posted on behalf of Alistair McTaggart, Postdoctoral Fellow, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria. Email: alistair.mctaggart@gmail.com

Web Pages: FABI profile (current employment), Google Scholar profileRust Fungi of Australia (taxonomy of rust fungi from prior post doc), Smut Fungi of Australia (taxonomy of smut fungi), Rust Fungi of Southern Africa (taxonomy of rust fungi in South Africa from current post doc)

Background

I am an early career researcher interested in the systematics of rust and smut fungi, which are both groups of plant pathogenic fungi. I dabble in the taxonomy of all other microfungi. I am currently based in South Africa and am being trained in genomics. I believe genomics is the best field to resolve the taxonomy and long-standing biological questions for my taxa of interest.

My answers largely reflect the field for taxonomy of fungi.


Where would you like taxonomy and systematics to be in a decade?

For pure taxonomy, I would like to see incorporation of new taxa into comprehensive, dynamic, public platforms, and an end to esoteric monographs. Taxonomy and application of a name should be accessible to everyone. This is possible through the development of public Lucid and Silverlight keys (here is an example of my friend Tim’s key to Carex in the United States: http://tinyurl.com/zjodnbb) that are open for collaboration within the community and are easy for non-experts to use. Single species descriptions are fine, but without incorporation into a bigger taxonomic picture, they pass by unnoticed. The community needs to embrace bigger picture treatments for their organisms. In the world of rust and smut fungi (and others), it’s already happening!

For systematics, I would like (and think it will happen) a total shift to phylogenomics, even if this means including a few loci of a taxon into a phylogenomic dataset. Cryptic species are rife in the mycological world and morphology only gets a taxonomist so far. Experts of a group rely on molecular barcodes and might not be able to make a confident identification of species (or genera) without molecular data. Mycologists have gradually progressed from single loci, to concordant and concatenated phylogenetic species hypotheses. Last year, we saw the first phylogenomic study of Zygomycota, which was casually published in a low-impact (but excellent quality) mycology journal. This will be the standard in the future. The sooner we get there, the sooner people will stop changing the taxonomy with every new gene they sequence. People working on genomic data will determine markers that may resolve a particular group, or markers that need to be included to determine populations, species, genera, families… The mycological community (at least) is going to have to embrace phylogenomics because this will happen within a decade (1K Fungal Genomes almost complete). This month I sequenced my first genome on a MinION (NanoPore™) with a desktop computer. In 10 years such a procedure will be less exciting for those taking part, and huge amounts of data will be at our fingertips.

What achievements or programs would you like to see in place?

Opportunities similar to the 1K Fungal Genomes project (or 10K Plant Genomes) for Australian taxa, particularly microorganisms.

High Performance Computing facilities made publicly available to researchers that need to work with large datasets (compare to the CHPC in South Africa).

Secure, electronic repositories to store genomic sequencing data before (and after) genomes are uploaded to public databases.

What innovations in technology, infrastructure, funding or organisation will make a big difference to your work and to our taxonomy and systematics?

  • Technology to sequence genomes from small amounts of starting material (such as Chromium 10X).
  • Desktop sequencing platforms (such as MinION).
  • Reduced cost of genome sequencing.
  • Access to electronic storage and high performance computing.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1184568 2017-08-18T00:40:57Z 2017-09-04T00:26:59Z Taxonomy 2028 Challenge: No net loss of FTE dedicated taxonomists

Posted on behalf of Dr Glenn Moore, Curator of Fishes, Department of Aquatic Zoology, Western Australian Museum


  1. By 2028 we will have no net loss of FTE dedicated taxonomists Australia-wide
  2. This will result in  security of taxonomic capacity and prevent the ‘brain drain’.
  3. This matters because there has been a well-documented global decline in dedicated taxonomists over the past few decades (eg Boero 2010; Disney 1998; Drew 2011).  This is despite the increasing need to understand the basic units of environmental, ecological, climate change and related research.  While much of the Decadal Plan is focussed on raising awareness of the role of taxonomy and its obvious importance to all fields of biological research, we also need to draw a line in the sand and stop any further reductions in taxonomic capacity in Australia.  We argue, with good reason, for increased staffing, training and students in the field, but this relies on increased funding.  The first step is to stop the decline, which already operates within funded models (at least to some degree).  Capacity needs to increase by 2028, but at the very least we must ensure it doesn’t decrease!
  4. Resources to achieve this will be recognition of the role of taxonomy, support from administrators, funding

Boero, F. (2010). The Study of Species in the Era of Biodiversity: A Tale of Stupidity. Diversity 2: 115.
Disney, H. (1998). Rescue plan needed for taxonomy. Nature394(6689), 120.
Drew, L. W. (2011). Are We Losing the Science of Taxonomy? As need grows, numbers and training are failing to keep up. BioScience61(12), 942-946.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1183755 2017-08-15T03:45:44Z 2017-09-04T00:30:21Z Taxonomy 2028 Challenge: Greater engagement with the public and end users of taxonomy

Taxonomy is a field that celebrates the immense diversity of life and allows for effective communication across not only scientific disciplines related to biology, but also for a whole range of other fields and industries that are crucial to our society (e.g. medicine, biosecurity, horticulture etc.). Its central role across these disciplines often goes unnoticed and in many cases underappreciated (e.g. Garnett & Christidis 2017). 

The level of success that we hope to achieve from our decadal plan (and indeed also with all subsequent plans after it) will invariably depend on the support of not only the systematic and scientific community, but also the larger community as a whole. Therefore, I propose that:

By 2028 we will achieve greater awareness, appreciation, and engagement from the wider public about the role and importance of taxonomy and systematics.

This will only result in outcomes that will inevitably benefit taxonomy and systematics which in turn contributes to the wider society. E.g. Greater funding (hopefully!) for taxonomic research and infrastructure development due to an increased appreciation and demand for taxonomic knowledge from the public.

Resources to achieve this will include:

First, broad surveys conducted during the start of the decadal plan followed by subsequent surveys at regular intervals (e.g. annually), allowing us to quantify and track our progress. Consultation and collaboration across the systematic society and social sciences would be particularly important in this case.

Similar initiatives have been noted, for example a survey was conducted during last year’s ASBS conference at Alice Springs targeted to our systematics community, and for botanical collections (e.g. the State Botanical Collection Significance Assessment, Royal Botanic Gardens Victoria 2016), though none has been conducted to the wider public at present.

With awareness comes appreciation, and with appreciation comes engagement – a crucial component for any endeavour. Questionaires can be constructed following this order:

1)   Awareness:

Example Q: Are you familiar with the fields of taxonomy and systematics? Y/N

Example Q: Are you aware of what a herbarium is? (*most people I’ve asked don’t!) Y/N

Example Q: Do you think herbaria and museums play a role in the fields of taxonomy and systematics? Y/N

Example Q: What do you think are the roles of a taxonomist or systematist?

2)   Appreciation:

Example Q: How important do you think the fields of taxonomy and systematics are to our society?

rank from 1–5 (for economic importance, scientific importance, cultural importance etc.)

Example Q: How important do you think the fields of taxonomy and systematics are in understanding and classifying the diversity of life?

rank from 1–5

3)   Engagement:

Example Q: Is the level of engagement of the taxonomic community with the broader public and end users sufficient?

rank from 1–5

Example Q: How can we improve our level of engagement?

The brief example above is targeted for the broader general public. Similar surveys can be created for specific groups of end users such as consultants, horticulturalists, or even other scientists who are not in the fields of taxonomy or systematics. Questions can be crafted following discussions and consultations with members of our community.

Establising a baseline survey will be critical in monitoring our progress. E.g. what percentage of the public is aware of the roles that taxonomists and systematists have?

In addition, these surveys will allow us to tailor our approach and invest in areas that we are currently lacking in terms of outreach (besides new species discoveries that attract the attention of the press and often quirky names that are associated with these new taxa [e.g. in Crisp et al. 2017], other roles of taxonomy often goes unnoticed – such as breakthroughs linked with evolutionary biology, phylogenetics, and biogeography).

Any potential differences noted across different levels of demography would be of particular interest  ­­–  especially on the responses of the younger generations (i.e. prospective and current students of biology).

Attracting and engaging younger generations in the fields of taxonomy and systematics is crucial to the survival of these disciplines. Engaging the younger demographic would require the use of media channels that they are regularly exposed to e.g. social media channels.

Noteworthy examples that utilises social media for taxonomic outreach include:

Novataxa: A blog dedicated to disseminating taxonomy and science, by featuring newly described species from across the planet in a way that is accessible to the wider public (by including pictures and summary diagnoses that can be understood by a layperson).

www.novataxa.blogspot.com.au

www.facebook.com/novataxa/

In other cases, personal blogs or social media sites (e.g. www.instagram.com/francisnge/) can also serve as an effective medium for taxonomic outreach.

Herbaria across Australia have their own dedicated social media sites on Facebook, and indeed one also exists for the Australian Systematic Botanical Society. Perhaps a site specifically dedicated to disseminating taxonomy and systematics should be created for the Australasian region, featuring the immense diversity that we have. A working model could include some of the features noted in Novataxa and In Defense of Plants ­­– a popular American botanical site aimed at engaging biology students (www.indefenseofplants.com; Fig. 1), it’s facebook site has garnered over 29000 likes www.facebook.com/InDefenseOfPlants/

Figure 1. Attracting a wider audience to what taxonomy and systematics entails – the study of the diversity of life.

A more active engagement from the public could aslo be achieved through these social media sites, for example the Kwongan foundation (www.facebook.com/kwonganfoundation/), a community site created for the conservation of Australia’s biodiversity with input from people across all regions, including those outside of Australia. Active participation from the community is maintained through engagement with other relevant groups that are present on social media e.g.

The Wildflower Society of Western Australia (currently with over 7000 online members; www.facebook.com/groups/129636970391772/)

and the Australian Native Plant Enthusiasts forum (currently with over 9000 online members; www.facebook.com/groups/675253642559682/)

Of course, engaging through the use of social media is only one way in getting our message across, and there are numerous ways of doing so, including increasingly novel ways that evolve with the development of increasingly sophisticated technologies (e.g. apps for plant identification). Nevertheless, it is a useful medium for which we can disseminate information through to a wider audience.

Finally, additional subsequent outreach strategies can be drafted, developed, and implemented following surveys conducted to the relevant stakeholders and consultation with the wider community.

Contributed to the Taxonomy 2028 Challenge by Francis Nge, University of Adelaide and State herbarium of South Australia

References:

Crisp, M.D., Cayzer, L., Chandler, G.T. & Cook, L.G. (2017). A monograph of Daviesia (Mirbelieae, Faboideae, Fabaceae). Phytotaxa 300(1): 1–308.

Garnett, S.T. & Christidis, L. (2017). Comment. Taxonomy anarchy hampers conservation. Nature 546 Issue 7656 (1st June 2017 ): 25–27.

 

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Francis Nge
tag:notobiotica.posthaven.com,2013:Post/1183174 2017-08-13T06:23:06Z 2017-08-24T02:56:21Z Taxonomy 2028 Challenge: a taxonomic emergency for vanishing coral reef fauna

The world’s coral reefs are facing imminent degradation from a variety of pressures. Current research suggests we have lost half of the world’s coral reefs in the last 30 years, and that reefs will disappear completely in the next 20-30 years. Despite this, the biodiversity of coral reefs is globally estimated to be represented by around 950,000 (±40%) multicellular species and only 10% of them have been described (Fisher et al. 2015). 

By 2028 we could double the number of described coral reef taxa.

This vision will result in a more comprehensive inventory for a fauna that we do not have the luxury of working steadily on for the next few decades. This is of great importance for a myriad of reasons, not least among which, coral reef organisms have contributed many new drugs that might preserve or improve human well-being.

This type of taxonomic emergency is something that scientists should come together to co-operate and speed up outcomes, before its too late.


[To be honest, I have no idea if this is achievable or not. It would require the description of 95,000 species in 10 years. Seems big. But achievable if big investment also occurs. And morally speaking, I think we should try!].


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Nerida Wilson
tag:notobiotica.posthaven.com,2013:Post/1181258 2017-08-11T07:55:38Z 2017-08-24T13:32:14Z Taxonomy 2028 Challenge: The Australian National Biodiversity Collection

Australia currently has around 100 public biodiversity collections (based on the ALA's Collectory pages), with a combined holding of >50 million specimens covering all organismic groups, and an estimated value of >$5 billion. In aggregate, the collection comprises a megascience infrastructure for biodiversity research in Australia, our region and the world, similar in scale and value to other megascience initiatives such as the Square Kilometre Array or the Large Hadron Collider.

However, the collection is jurisdictionally very scattered. In general, each state and territory has a large or relatively large herbarium and museum collection, under a variety of jurisdictional and reporting arrangements (e.g. from semi-autonomy under an independent Board to embedded in botanic gardens or various government departments). Some universities have collections, ranging from small teaching collections to substantial holdings. There is also a long tail of smaller, special-purpose collections in universities and various government departments. 

This jurisdictional scatter has arisen for obvious historical reasons: the establishment of the major herbaria and museums was mandated or facilitated under state and territory legislation; the CSIRO collections were established under its research mandate; and the smaller collections were established by universities and government departments for specific purposes not adequately covered by the major institutions.

Importantly, funding decisions that affect our collections are made by a very wide variety of budgeting agencies (from local to state or territory to national), with very little national coordination or strategy that can buffer a given collection from the exigencies of its local funding pressures.

Further, the wide scatter of collections means that few "owners" of collections see their collection as part of a megascience infrastructure, and nor does the community as a whole.

So, here's my vision:

By 2028, all our biodiversity collections will be integrated to form the Australian National Biodiversity Collection

The main goal of the ANBC will be to change the way governments, industry and the community view our individual collections - from seeing them in isolation to seeing them as part of something much greater. For obvious reasons, each individual institution will remain under local jurisdictional control and management. However, we will market our collections as e.g. "The xxxx collection, part of the Australian National Biodiversity Collection". 

We will establish an arrangement under the Council of Australian Governments (COAG) whereby the importance of each collection as part of the whole is acknowledged, including if possible negotiated agreements on minimal required baseline funding for each collection. 

We will also establish a strategic governance structure for the ANBC as a whole, to ensure strategic planning for the aggregate as well as individual collections, rather than for individual collections alone, and to increase recognition of the strategic value of each collection and of the ANBC in aggregate, in order to increase profile and funding.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1180425 2017-08-04T11:28:10Z 2017-08-31T04:12:50Z Taxonomy 2028 Challenge: Providing certainty in taxonomic applications through next generation sequencing

Holotypes are the universal standards we use to build our taxonomic knowledge. Since the integration of genetic data into our methods, our knowledge of diversity is rapidly increasing, but rarely can be linked back to species names. This has led to a divergence of knowledge systems where sometimes we have a parallel set of understanding that cannot be accurately tied together. In order to progress taxonomy, we need to be able to link all this new information with the centuries of foundational work based largely on morphology. Most holotypes are old, or preserved in a way that doesn’t easily allow the extraction of genetic information. However, newer technologies have overcome many of these issues (e.g. formalin preservation, degraded samples) and it should be possible to retrieve a barcode that could link historical type material with molecular studies.

By 2028 we will barcode 50% of holotypes in Australasian collections. This will result in the ability to link genetic information with available names and provide context for interpreting all molecular studies. This will solve some seemingly intractable taxonomic questions, and provide an essential resource for the future. This matters because currently, at best, molecular studies can include material re-collected from type localities, but most don’t, or can’t, since these areas may be highly impacted by human development. The proposed project will provide absolute certainty for contemporary identifications.

While it is not possible to utilise a single gene across all life, the key is unlocking the relevant marker for the groups of interest. Shotgun sequencing can be used to produce barcodes for type material. Shotgun sequencing breaks up DNA into small pieces, which get sequenced in short, overlapping fragments. These are assembled into continuous pieces, which will usually contain the high copy genes that we often use for species-level studies.

By maintaining project-level hubs at the involved institutions, existing databases will maintain the complete metadata record, while a purpose-built (very simple) database could list the species name and collection registration number. Using these two terms in a search of the public database GenBank, where data will be deposited, will retrieve all available data for that type. Other resources required would be salaries for project managers/scientists, a budget for sequencing, and the support of the involved institutions.

This project will increase the utility and integration of existing genetic information and provide absolute certainty of species-level identifications. It will also reduce the need for loaning or handling type material, which in many cases, becomes more fragile with age. This is future-proofing taxonomy!

By Nerida Wilson and Kym Abrams

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Kym Abrams
tag:notobiotica.posthaven.com,2013:Post/1180331 2017-08-04T03:39:32Z 2017-08-04T03:39:32Z Taxonomy 2028 Challenge: Life in the Late Anthropocene

Here's a wild idea for the Taxonomy 2028 Challenge - some thoughts that came from listening to Peter Raven's talk about the Shenzhen Declaration at the recent International Botanical Congress.

There are two possible scenarios for the future of humankind in the Anthropocene:

Scenario 1: we catastrophically over-reach the earth's carrying capacity, resulting in an uncontrolled crash back to a pre-industrial state (from which we will probably never fully recover given that all the easily accessible fossil fuels are now used up);

Scenario 2: we manage the coming demographic transition in a sustainable way, with population (and resource utilisation) peaking sometime mid-Century followed by a gradual decline in both population and resource use, and with continued increase in our technological capacity.

In either scenario, the Anthropocene will inevitably comprise a mass extinction event. In the first scenario, the living world will come through the mass extinction in much the same way as it has in the past, with diversity gradually rebuilding over the next several million years. 

In the second scenario, we have a more interesting (and optimistic) scenario. After the demographic transition, we will be able to gradually reduce our ecological footprint, and will be able to embark on a phase of "rewilding" the planet - we contract the amount of land we need for food production as we farm more intensively and technologically for a smaller population, which makes land available for restoring wild spaces and the ecological services these provide.

The problem is, we will have lost a significant amount of biodiversity by the time we can start the rewilding.

So here's the proposal:

By 2028 we will have collected and stored tissue samples from all Australasian biota in a genomic ark

Despite the inevitable mass extinction, we act now to store as much genetic diversity as possible in the form of DNA-stable tissue samples. Once the rewilding starts, we will almost undoubtedly have the technological capacity to recreate species from DNA samples, using CRISPR/Cas9 or other gene editing technologies. The limiting factor will be having the DNA material to do this.

So, by 2028 we will have an Australasian genomic ark, the main purpose of which (though not the only purpose) is to store stable genomic samples of as many organisms as possible from our region. This can be done in a variety of ways, e.g. dried leaf samples for plants and tissue samples for animals, environmental samples for fungi, microbes etc.

An interesting issue is that we need to try to sample as much biodiversity as possible including currently unknown taxa. The taxonomy can come later (perhaps even after the rewilding) - we don't need to have the taxonomy all worked out before we sample. We should aim to store as many tissue samples as possible, whether the know what the organism is or not. This has interesting implications for the sampling strategy we would employ for this.

Such an ark could become an absolutely invaluable resource in the future (if we can avoid scenario 1).

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1180326 2017-08-04T02:52:18Z 2017-08-18T01:20:54Z Taxonomy 2028 Challenge: Palaeobotany for future planning Posted on behalf of Prof. Bob Hill (University of Adelaide), with help and contributions from a broad sector of the Australasian palaeontological community
By 2028 we will have a totally integrated record of fossil and living plants in Australia in a way that allows for the fossil pollen and spore record (microfossils) and the record of macrofossil remains to be linked as strongly as possible from the perspective of their taxonomic identity. This, along with the age and location of the fossils, can then be overlain on the current knowledge of living plants species and their distribution to demonstrate that the unique island laboratory that is Australia can be reconstructed vegetatively in a way that is unachievable elsewhere on Earth. 

Australia is unique in being a large, flat and mostly isolated land mass that has not undergone any major environmental upheavals for tens of millions of years except for climate change (and some coincidental changes in photoperiod and light availability). The plant fossil record is much larger than most people realize and it offers a stunning record of the change in vegetation that is about as extreme as it is possible to imagine for much of the continent (often from dense rainforest to arid desert). A full reconstruction of this would be an amazing achievement, and would highlight the precious nature of the Australian biota and its journey over millions of years. 

This work will result in a data base that will allow for sophisticated reconstructions of the past impact of climate change, the arrival of humans, changing fire regimes and much more. In the best case this will play directly into matters of significant community importance like planning for future climate change and best managing fire into the future. On another level it will provide researchers with unparalleled access to fossil data when utilizing the living flora for detailed evolutionary studies. Taxonomically well-validated fossils are critical for such studies, and are increasingly showing that molecular-derived dates of lineage divergences are often much too young. There is also potential amongst more recent fossils for ancient DNA and chemical fingerprinting of both micro- and macrofossils to better separate out genera and species. Overall this contributes to a stronger integration of the fossil vegetation record with the extant vegetation. 

All this matters because Australia has undergone extreme change in the past 40 million years and is highly vulnerable to future change. By increasing our level of understanding of the past and how it has shaped the present, we stand a better chance to influence what the future might look like. 

Resources to achieve this include smart young researchers who are committed to their own, but also to the collective, good. None of the research required here is expensive, but it needs a new generation of people with research skills that are fast disappearing. It also requires a very sophisticated databasing approach and firm overall control so that data is compatible across all areas. The approach taken should match that used for databasing the living Australian vegetation, but will include the need for better access to modern microscopy (scanning and transmission electron microscopy), automontage microscopy and some of the newer techniques for analyzing specimens such as neutron tomography, which is available at ANSTO. 

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1180324 2017-08-04T02:45:16Z 2017-08-18T01:24:05Z Taxonomy 2028 Challenge: Every Australian species genomed (is that even a verb yet?)

Posted on behalf of Dr Peter Johnston, LandCare Research, New Zealand


By 2028, every species in Australasia has had its genome sequenced. 

This includes named species, as well as species known from specimens or living cultures in curated scientific collections, but not formally named.

The IT infrastructure needed to manage this data, analyse it, interpret it, and deliver it in a way that is useful to humans, is available. This interpreted data will be delivered to users in real time and updated as new taxa are discovered.

This will provide:

  • a truly robust phylogeny of Australasia’s biota, from population through to kingdom.
  • understanding of the Australasian species and lineages that make this part of world special, irrespective of kingdom [e.g. from koala to epacridaceous root endophytes]
  • recognition of the species and linaeges that are exotic, prediction of their putative biology, and understanding of their potential risk to Australasia’s economy and inidigenous biota.
  • ability to place taxa known only from environmental DNA sampling in the phylogeny, irrespective of the gene or genes used for that sampling.
  • important management tool for dealing with the high-risk and unique parts of Australasia’s biological diversity through accurate mapping across space and time, based on national landscape-scale eDNA surveys. 
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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1179998 2017-08-03T08:30:51Z 2017-08-04T02:57:54Z Taxonomy 2028 Challenge: Microbial diversity

 Using the potential of microbial diversity in innovative ways:

By 2028 we will be in the age of microbiology, with micro-organisms contributing to the majority of industrial processes.  We urgently need to explore their diversity and potential. 

This will result in using microorganisms and their enzymes to improve human health, increase crop yield, recycle waste products and eventually replace much of the fossil(ised) economy.

This matters, because with an increasing population and increasing demand for animal protein, agriculture must become more efficient, as there are finite resources on earth there is an urgent need to reduce or recycle waste, and a moral requirement to reduce pollution from industry.

Resources to achieve this will be

·         Public support so that people are aware of, and in agreement with, using microorganisms and their enzymes to ensure a more sustainable future.

·         The political will to look forward, by investing in discovery programmes focussed on the microbial communities of Australia in ancient rocks, in highly leached soils, and from the unique flora and fauna that occurs in diverse climatic regions.  These programmes will include not just what is there, but how these organisms are able to survive in such unusual environments.  An outcome with be to determine how this ability can be exploited in novel ways in new industries.

·         Investment from the extractive industries in microbial discovery in low pH and highly saline environments in order to develop enhanced biomining and bioleaching of mineral ores.  This will enable these techniques to be applied to a wider range of materials, under a greater range of physical condition than is possible at present.

·         Investment from the agricultural industries for developing microbial products for the better use of waste products.  An example is the use of fungal enzymes for recycling keratin from animal waste into nitrogen-rich products such as plant fertiliser and animal feed.

·         Investment by manufacturing industries in the use of microbial enzymes to minimise waste and pollution, so that this becomes part of their licence to operate.  Examples are the use of fungal enzymes in the pulp and paper industry, and in tanning leather.

 

This list could go on….and on….


Elaine Davison


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Elaine Davison
tag:notobiotica.posthaven.com,2013:Post/1172075 2017-07-10T05:08:22Z 2017-07-10T05:08:22Z The Taxonomy 2028 Challenge - Shaping the future of biosystematics and taxonomy in Australasia

You’re invited to take part in the Taxonomy 2028 Challenge, to help create a vision for systematics and taxonomy in Australasia for the coming decade.

We’d like you to scan the horizon, and share what you see. Where would you like taxonomy and systematics to be in a decade? What achievements or programs would you like to see in place? What milestones would you like us to pass? What innovations in technology, infrastructure, funding or organisation will make a big difference to your work and to our taxonomy and systematics?

An inspiring and ambitious vision for the future is a key element of the Decadal Plan for Biosystematics and Taxonomy in Australasia 2018-2028, which is currently under development (see https://www.science.org.au/support/analysis/decadal-plans-science/biosystematics-taxonomy).  

In thinking about this, please think in concrete terms. We’re after ideas that, after discussion and with broad community consensus, can be included in the Plan as specific objectives (such as projects, programs or milestones of activity) that will benefit both our science and our end-users. We will use these as hooks to argue for more resources, to create more visibility for our discipline, and to foster a more general appreciation and understanding of the value of taxonomy and systematics.

We also need to build the foundation for the next decade (2028-2038), so please think ahead.

The Taxonomy 2028 Challenge will work as follows. Please write a description of your idea. This should be fairly concise if possible, but your contribution could be a couple of lines, a paragraph, some dots points, a blog, or a full-blown discussion paper. Ideas cannot be too big, or too small (though we prefer big). If you have lots of ideas, please write separate pieces for each, unless they go together as a package. There’s no limit to the number of contributions per person.

In order to keep some consistency, please try to structure your contribution something like this:

  1. By 2028 we will … [the big idea]

  2. This will result in  …., …., …. [the impact]

  3. This matters because …., …., …. [the importance]

  4. Resources to achieve this will be …., …., …. [the details]

Please try to think in the context of your own work and research group, but also outside to biodiversity in general - the Plan, after all, will cover all of biodiversity. Goals such as “By 2028 we will develop a complete phylogeny of all [.....] in a cool genus beginning with C” may be a little narrow in scope.

It’s probably a good idea to discuss your ideas with colleagues and friends, either before or after you write the first draft.

When you’re ready, please email your contribution(s) to me at kevin.thiele@science.org.au. Indicate in the email whether you’re happy to be publicly acknowledged, or would prefer to remain anonymous.

All contributions will be published on noto|biotica for comment and discussion as they come in. At the close of the Challenge, we’ll analyse all contributions for common themes, and use them for further discussions including for sector meetings later in the year. All contributors will be acknowledged in the final Decadal Plan.

We’re very keen to hear from as many people in our sector as possible; so, whether you’re paid staff, volunteer, associate, or student, whether you work directly in taxonomy or biosystematics, or in associated roles such as curation or bioinformatics, please put your thinking caps on.

We’re also very keen to hear from students and Early Career Researchers (after all, it’s your future we’re talking about). As encouragement, three prizes are up for offer, to a student or ECR who contributes the:

  • most popular idea

  • most novel idea;

  • most ambitious vision.

CSIRO Publishing is dedicated to publishing excellence in taxonomy and systematics, and has generously offered a prize for the winner of each category above. The prize consists of a $100 book voucher, as well as a subscription to your choice of journal (Australian Systematic Botany or Invertebrate Systematics) and free open access for your next publication to one of the above journals. Prizes will be judged for contributions received before 31 August 2017.

So – please do the vision thing, and let’s start shaping our future.

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1159860 2017-06-06T03:50:38Z 2017-06-09T04:30:04Z Why Australia's plant phrase-naming system is more interesting than it seems (Part 2)

In Part 1 of this blog (please read that first if you haven't already) I established (I hope) that the system we operate in Australia for phrase-naming vascular plants is an interesting and noteworthy initiative, and one that could perhaps be extended and explored as one part of a solution to the taxonomic impediment (the name we give to the problem that there are not enough of us and we don't have enough time to name all the organisms we need to name). 

I made a claim that the phrase-naming system has all the requirements to be regarded as a Controlled Namespace, and in fact runs parallel to, and augments, that other great controlled namespace, the International Code of Nomenclature for algae, fungi and plants

The purpose of this blog is to make two arguments, firstly that we should consider extending the phrase-naming system to all biota, and secondly (and probably more controversially) that we should explore using it to name aspects of biodiversity that are worth naming, but may not be "taxa" (whatever they are).

Extending the phrase-naming space to all biota

Botanists in Australia created their formal phrase-naming system for two reasons. Firstly, we inhabit a mega-diverse country with a partially documented biodiversity, and are all aware of "good" taxa that, despite not yet having a formal name, nonetheless are in need of recognition and protection. Secondly, and because of this, at the time we commenced work on the Australian Plant Census (APC) project, it became clear that if we included only formal names, we would mis-estimate our plant biodiversity. An intent of the APC was to harmonise taxonomy across state borders, and harmonising phrase-names is just as important as harmonising formal names. In these senses, the phrase-naming system is a simple solution to a practical problem.

The problem that we faced is not unique to botany. In many other taxonomic groups, we recognise more taxa than have yet been named. Collections with large numbers of un-named species are often partially curated using taxonomic "sorts", either physically in the collection, electronically in databases, or at least in the minds of the curators. If an important task of taxonomy (arguably the most important) is to document all known biodiversity, then these "sorts" represent documentation that's currently pretty undocumented.

A practical problem with documenting these undocumented taxa is that they are currently (except for plants) named using Locally Controlled Namespaces, or worse, Completely Uncontrolled Namespaces. If something in a collection is called "Fly sp. 1", there's not much to go on for anyone trying to understand the taxonomic concept concerned. If another collection also has a "Fly sp. 1", and if there's reason to believe that "Fly sp. 1" ≠ "Fly sp. 1", then we have a problem. This is exactly the problem that GUIDs (taxon or phrase-names) are designed to solve.

Just as with plants, capturing and rationalising these names so that we can assert (likely) equivalency between specimens having the same phrase name would be an enormous step in our task to document Australasia's biodiversity. It would give us an opportunity to capture all our knowledge, rather than just the part that's made it through all the hoops to formal naming.

Of course, this statement will immediately raise an objection in the minds of some readers. How can we be sure that these phrase-named taxa really are taxa, if we haven't yet done the taxonomic due diligence that comes with formal naming. An answer is that we work on a sliding scale, and we can't really assert anywhere along this scale that we're absolutely sure that taxon x is really a taxon. There are many cases where we can be as confident that an un-named taxon is a good taxon, as that a named taxon is a good taxon. While there will always be some uncertainty, I don't think we should let that stand in the way of a more efficient and effective way of documenting our biodiversity. 

So - I propose that, as one of the initiatives under the Decadal Plan, we extend the formal phrase-naming of Australasian taxa to all biota, and that we initiate a campaign to capture all of our current taxonomic knowledge, including knowledge that for various reasons hasn't yet made it through to formal naming. The following steps would be needed:

  1. the adoption of a single agreed convention for phrase-naming informal taxa throughout the biota (I'd like to propose the vascular plant phrase-naming convention as a bloody good start);
  2. the initiation of a campaign to capture within the agreed phrase-naming system all taxonomic knowledge represented in our collections and data systems; and
  3. commencement of a system of rationalisation between collections so that over time we can be confident that the same phrase names apply to the same taxa throughout.

Extending the phrase-naming space beyond taxa

I've described the current vascular phrase-naming system as being akin to a parking lot for taxa that await formal naming. This need not necessarily be the case, however. 

If, as I argued in Part 1 of this blog, a phrase-naming system is effectively a Fourth Namespace that sits alongside and parallel to the three existing nomenclatural Codes, it follows that we could design that namespace to do whatever we want it to do. If there are cases where we'd like to name something (i.e., do taxonomy) but we believe this is best dealt with outside the Codes, then we can design a controlled namespace from scratch and optimise it to deal with these cases.

This is where my idea of an all-biota phrase-naming system may get controversial, and I may get shot down.

Nature is immensely complex. Evolution has generated patterns of variation that are among the most challenging in the universe. Given this, is it likely that a one-size-fits-all approach to naming this pattern (one or other of the Codes depending on one's organismal group) is going to be adequate for the task?

Consider genetics and genomics. These immensely powerful tools allow us to discern patterns at a level of resolution and detail never before dreamed of. Having discerned a pattern, there's a strong desire among those of us with a taxonomic bent to want to name entities that we can discern from the pattern. If only one controlled namespace is available, that's the one we choose to name under. I think there's a danger here - that we'll bugger-up a perfectly good naming system that can't, or shouldn't, need to cope with all this extra detail.

This is one reason why I worry about "cryptic species" (I put the phrase in quotes because too often it's written without, thus rather prejudging the whole issue). Let's say that we have a lineage that's morphologically recognisable. Let's say that it was a species that currently has a name (probably dealt with using classical methods). Let's now say that genetic and genomic studies reveal well-characterised sub-lineages, which are not currently recognised in our taxonomy. Having discovered these cryptic lineages, we're tempted to name them as "cryptic species". 

This is all well and good if the point of naming is merely to document biodiversity by boffins, for boffins. The problem is that there are many more non-boffins than there are boffins, and many of these comprise "the public". I believe we ignore this at our peril. Jenny Citizen used to be able to recognise this species, but is now faced with half-a-dozen "cryptic species" that she can no longer discern. If our naming system gets loaded with taxa that she can't understand and can't see, then we'll lose her to our cause. This, of course, would be dangerous to our cause.

If there were only a small number of these awkwardly cryptic taxa, then the system would probably cope OK. If however, there are many, then loading up our taxonomy with names that are effectively useless for many (though not all) users, is a problem. My fear is that the more we look, the more cryptic variation we'll find.

And this is where the Fourth (or Fifth, or Sixth) Namespace comes in. We could design a namespace that's optimised to allow us to capture names of things (such as morphologically cryptic lineages) that we choose not to name in our Code-based namespace. Because our new namespace is a controlled one, it would still serve perfectly well for communication among the boffins and other rare breeds who need it. Our Code-based namespaces, which perhaps are more public-facing, could then be immune from being over-stuffed with these things. 

This would also have the advantage that we'd solve a current problem even for us boffins. Many researchers who discover lineages (or sub-lineages) using genetic and genomic methods, fail to name them under the Codes because they find it too hard. There's a curiously anachronistic view around that you need to find some morphological difference (any morphological difference) to be comfortable to name something under the Codes. A result is that some people work away trying desperately to squeeze some minor morphological difference out of their poor creatures, then (if they get lucky) name them on that basis. Others either give up, or don't bother. The result? Our worst enemy - an uncontrolled namespace. How many Clade A's can you think of in your group's literature? We could invent a system that works better than this.

So - I propose that we investigate a phrase-naming system that will allow us to name genetic lineages and other entities that should be named, just not under the Codes.The following steps would be needed:

  1. the adoption of an agreed convention for phrase-naming genetic lineages (and perhaps other entities such as significant populations);
  2. the establishment of standards for journal papers that will provide a convenient way for such names to be coined; and
  3. the establishment of a system to track and document these names, and that would allow them to be resolved back to an original source.

We could then inhabit the best of all possible worlds (well, that might be going too far), with several carefully controlled name-spaces each optimised for different uses. The sum of our taxonomic knowledge would be the sum of these namespaces, in whatever combination is most fit for purpose for the particular questions asked. I think this would give us much-needed flexibility, that is currently lacking in our nomenclatural system.

Over to you for comment...

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1141564 2017-06-05T07:07:27Z 2017-09-12T00:18:12Z Why Australia's plant phrase-naming system is more interesting than it seems (Part 1)

For the last decade or so, Australian botanists have been doing a very interesting thing (we've actually been doing lots of interesting things, but this blog is about just one of them). We’ve been naming taxa (or at least, putative taxa) outside the International Code of Nomenclature for algae, fungi and plants (the Code), using a parallel but carefully formulated and controlled nomenclatural system.

This is the phrase-naming system, standardised by Bill Barker on behalf of the Council of Heads of Australasian Herbaria (CHAH) in 2005 (see Barker, W.R. Standardising informal names in Australian publications, Australian Systematic Botany Society Newsletter 122, 11–12, 2005).

A phrase name is a name constructed under the agreed CHAH standard, with the form “Genus-name sp. Phrasename (Voucher specimen identifier) Source”. Some examples are Acacia sp. Ambathala (C.Sandercoe 624) Qld Herbarium, Sauropus sp. Jabiru (C.R.Dunlop 3381) NT Herbarium, and Typhonium sp. Kununurra (A.N.Start ANS 1467) WA Herbarium.

The phrase-naming system was standardised at the time the Australian Plant Census (APC) project was initiated. This is no coincidence – the APC was an initiative to checklist accepted vascular plant taxa across Australia, and a standardised phrase-naming system was required for that effort.

At first glance, our vascular plant phrase-naming system may seem prosaic and uninteresting - what's so special about putting tag names on plants? However, I reckon it's actually much more interesting than it seems. Firstly, to the best of my knowledge, it's globally unique: no other country has an agreed, formal, multi-jurisdictional standard for naming taxa outside the normal provisions of biological nomenclature. But beyond it's uniqueness, I think it establishes a precedent and a model that could provide much-needed flexibility in naming throughout modern taxonomy and systematics.

Names and namespaces

Technically, names are GUIDS (Globally Unique Identifiers). A GUID is a key (a number or text string) that identifies a thing, and that the system designer can assert uniquely identifies that thing and only that thing within the system. If this is the case, a GUID can then stand in for the thing itself. GUIDs are particularly important in globally distributed systems (like the internet, or biology), where the Globally Unique part of GUID means exactly that.

To ensure that GUIDs are globally unique, a control system and a set of rules are needed, which together control the assignment of GUIDS to things, and the resolution from GUIDS to things. If such a control system is present, and it results in global uniqueness, the system is called a Controlled Namespace. A great example of a controlled namespace is the DNS (Domain Name System), which controls how domain names (like notobiotica.posthaven.com) are assigned and managed. If the DNS didn’t control domain names as GUIDS, and two separate websites could each have the same domain name, the internet would quickly unravel.

Taxonomists around the world are very familiar with controlled namespaces, because that's what the three Codes of Nomenclature (the botanical, zoological and bacteriological Codes) are. The Codes are complex sets of rules that control how names are assigned (rules of validity), are deemed to be correct or incorrect (rules of legitimacy), and are resolved when several valid and legitimate options exist (rules of priority). The rules ensure that one taxon has one valid and legitimate name (that is, each taxon has a GUID). 

The Codes, while exceedingly important, are not perfect, largely because they evolved at a time when controlling the biological namespace was effectively impossible. Taxonomists wore funny wigs, spoke Latin, printed their taxonomy in books using Gutenberg presses, and distributed them by slow boat or a new-fangled and very cool thing called a postal service. If the internet had been invented at that time, it would be a complete mess. The fact that biological nomenclature isn’t a mess (it’s actually pretty good) is testament to the great workarounds that our nomenclatural forebears put in place at the time the Codes were consolidated in the late Nineteenth and early Twentieth Centuries.

As well as being imperfect, the Codes are not magical: they're useful only because of the controlled namespaces they enable. And if good reasons emerge to set up more controlled namespaces, there's nothing to stop us doing just that.

The fourth namespace

This is why I think the Australian phrase-naming system is interesting. It's a fourth controlled namespace. (Remember that it combines a standard rule for forming names, and a process - the APC - that ensures uniqueness, hence the phrase-name system in a formal sense is a controlled namespace.) In fact, while we often call phrase-names "informal", in contradistinction to the "formal" names created under the Codes, in many ways they're just as formal. 

This fourth namespace was created to solve a specific problem in Australian botanical taxonomy, which is that we have a bottleneck: taxa (at least, putative ones) are being recognised in Australia faster than we can deal with them under the normal mechanisms of taxonomy and name them under the Codes. The phrase-naming system was invented as a "parking bay", to enable names to be given to these taxa - with all that that implies for communication, conservation etc. - while they await "formal" naming. It's a neat partial solution to the taxonomic impediment, which of course is what causes the bottleneck in the first place. 

The thing I find interesting about this is that there are many dimensions to the taxonomic impediment, and formal phrase-names established under a controlled namespace, like the Australian vascular plant phrase-naming system, could play a larger role in dealing with these. In a later blog I'll try to draw out some of these possibilities, and to show that this fourth namespace could play a larger and more interesting role in our overall taxonomy than it does at present. It could, for example, be extended to the whole of Australasian biology, allowing the formal (informal) naming of organisms other than plants. In doing so, it could play an important role in rapidly capturing, with unique names, all our taxon concepts, even those that are not yet ready (for a variety of reasons) for naming under the Codes (or indeed, and here's a thought, ones that we have no intention of naming under the Codes).

Coming up next - extending phrase-names to the whole of life, and to more than just "taxa"...

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Kevin Thiele
tag:notobiotica.posthaven.com,2013:Post/1160722 2017-06-05T04:22:24Z 2017-06-05T05:05:06Z Darren Crayn A long time ago, in a city far, far away... I began engineering studies.

It seemed a logical choice at the time. For a boy growing up with a sciency bent in a small and unremarkable country town in northern New South Wales, it seemed engineering as a career made sense, or so said my rather unimaginative high school careers advisor. Off to the big smoke I went, and 6 months into a chemical engineering degree, I fell in love with .... biology.

Engineering and I negotiated an amicable separation and my new crush led ultimately to a postgraduate degree at the University of New South Wales (Sydney), where I developed research skills and credibility in phylogenetic systematics of plants. After graduating I was off overseas where I worked on the evolution of photosynthesis in bromeliads, using a phylogenetic approach, at the Smithsonian Tropical Research Institute in Panama and Oxford University in the UK.

I returned home to Sydney in early 2000 and after a period of research odd-jobbing (ranging from taxonomically revising a small genus of vascular plants, to working on the genetics of gestational diabetes), I landed dream job #1: Tropical Botanist at the National Herbarium of NSW. A hugely satisfying 6 years of research and practical herbarium taxonomy ensued, until as fate would have it dream job #2 emerged, fully formed, seemingly from nowhere. Strange how the most wonderful things happen when you least expect them.

Dream job #2 is what I do now: Director of the Australian Tropical Herbarium, a joint venture between CSIRO, the Queensland Government, The Australian Government Dept. of the Environment, and James Cook University. This dynamic and growing organisation, located on JCU’s Cairns campus, aims to be a significant global player in tropical plant biodiversity research. My role is roughly equal parts management/leadership and research. The latter involves studies of the origins, evolution and classification of plants and deals broadly with the questions: how many plant species exist, where do they occur, how are they related and how have they evolved? More specifically this research is:

•       discovering, naming and classifying new plant species and determining the evolutionary relationships among them,

•       mapping the distribution of ecosystems, species and genetic variation within species across the landscape,

•       developing DNA-based tools and ‘matrix keys’ for species identification and rapid biodiversity inventory

•       uncovering the deep-time origins and ancient migration pathways of plants that are found in tropical Australia today

I’ve been lucky enough that research has taken me to many biomes and countries including the Republic of Panama, Venezuela, Papua New Guinea, Indonesia, New Caledonia, Malaysia, New Zealand and the United Kingdom.

In addition to institutional and science community leadership and research roles, I contribute to biodiversity and science policy development and implementation through roles on a number of advisory committees and expert panels for the Australian and State governments, and the non-governmental research sector.

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Darren Crayn
tag:notobiotica.posthaven.com,2013:Post/1160718 2017-06-05T03:31:58Z 2017-06-08T23:29:56Z David Yeates

I am an insect systematist and Director of the Australian National Insect Collection.  I hold an adjunct Professorship at the Australian National University and am also the Schlinger Curator of Diptera at ANIC.  After a stint as Roosevelt Postdoctoral Fellow at the American Museum of Natural History in New York, I returned to Australia teaching systematic entomology at the University of Queensland.  Not long after the Department of Entomology was amalgamated into a larger department at UQ I moved to Canberra to begin work as a research scientist at the Australian National Insect Collection.  I became the Director of ANIC in 2012.

My main interests are in the systematics and taxonomy of insects in general, and flies (Diptera) in particular, with special interest in Australian flies.  I have always had a strong interest in teaching and outreach, and promoting the importance of the work that taxonomists do.  Way back in my career I worked with Kevin Thiele to develop the Lucid system of interactive keys.  My current work includes molecular phylogenetics of insects, flies and various families of flies including the Bombyliidae (bee flies), Therevidae (stiletto flies), Stratiomyidae (soldier flies), Fergusoninidae, Tachinidae (bristle flies) and Tabanidae (horse flies), all done in collaboration with PhD students and postdocs.  I also teach undergraduate entomology at the Australian National University. 

Australia is an amazing place to be an invertebrate systematist.  With most of the fauna undocumented there are major discoveries to be made just outside every laboratory.  Because of the deep time history of Australia, and its preservation of habitats that have disappeared elsewhere on earth, very old lineages still find a home here.  In addition, due to the dramatic climatic changes in Australia through the last 60 million years, many groups have responded by radiating rapidly into new habitats. This combination of arks and cradles of diversification create compelling foci for taxonomic, systematic and evolutionary studies.

My research career has seen the advent of single gene molecular systematics, then through the dark days of multilocus molecular systematics using Sanger sequencing, and am now very pleased to have emerged into the light of high throughput sequencing (HTS).  Now various approaches can be used to assemble datasets that contain a very large portion of the genome through transcriptome sequencing and genome reduction techniques such as hybrid enrichment.  I am very excited about the promise of HTS for extracting large chunks of the genome from museum specimens, adding another important dimension to the value of biological collections.

Systematic entomology has an important role to platy in biosecurity within the broad scope of food security.  Because of its isolation, and strong biosecurity processes, Australia is free of many of the world's most devastating pests and diseases.  This has multiple benefits for our industries in terms of lower production costs, and access to premium markets overseas. In order for these benefits to continue, Australia needs to build and maintain capability in diagnosing the groups that pose a biosecurity threat.  We also need to be able to quickly distinguish the threats from the native fauna.  In many cases this is not trivial - Australia is home to large numbers of species that are very often challenging to distinguish from invasives.  This brings an important economic dimension to entomological systematics.

I have written a couple of pieces for the Conversation relevant to this blog site:

Why so many Australian species are yet to be named?

Australia: riding on the insects back

Hidden housemates: we live with a zoo of harmless mini-beasts

Insects are the great survivors in evolution



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